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Merge pull request #2235 from FedeGueli/patch-15
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Update lineage_notes.txt
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@AngieHinrichs
AngieHinrichs committed Aug 31, 2023
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2 changes: 1 addition & 1 deletion lineage_notes.txt
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Expand Up @@ -1483,7 +1483,7 @@ FB.1 Alias of B.1.1.529.5.3.1.1.1.1.1.2.1.1 S:D253G, Singapore/Taiwan/Japan From
FB.2 Alias of B.1.1.529.5.3.1.1.1.1.1.2.1.2 S:478R, USA/South Korea/Mongolia
BQ.1.2.2 Alias of B.1.1.529.5.3.1.1.1.1.1.2.2, S:K147E, S:R346T, S:V445A, West Africa from #1861
JH.1 Alias of B.1.1.529.5.3.1.1.1.1.1.2.2.1, S:K182E, S:486A, S:S494P, S:E554K, from #2068
JH.2 Alias of B.1.1.529.5.3.1.1.1.1.1.2.2.2, S:A484T, S:V486A, USA/Canada/Finland, from #2068
JH.2 Alias of B.1.1.529.5.3.1.1.1.1.1.2.2.2, S:A484T, S:V486A, USA/Canada/Finland, from https://github.com/sars-cov-2-variants/lineage-proposals/issues/650
BQ.1.2.3 Alias of B.1.1.529.5.3.1.1.1.1.1.2.3, E:V24L, Canada
BQ.1.3 Alias of B.1.1.529.5.3.1.1.1.1.1.3, found globally, defined by S:E619Q, from issue #1082
BQ.1.3.1 Alias of B.1.1.529.5.3.1.1.1.1.1.3.1, C2509T, Spain
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6 comments on commit 2351b67

@FedeGueli
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There is also S:A484T instead it is S:A484K but i would like to know if it is a mistake from reading Usher or a thought about it was initailly S:A484T by @corneliusroemer before PR for it.

@AngieHinrichs
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I believe it is S:A484T. Omicron has A23013C (S:E484A), and then JH.2 gets G23012A which changes amino acid A (GCA) to T (ACA).

@FedeGueli
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@FedeGueli FedeGueli commented on 2351b67 Sep 3, 2023 •
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I believe it is S:A484T. Omicron has A23013C (S:E484A), and then JH.2 gets G23012A which changes amino acid A (GCA) to T (ACA).

Ok i will tell @ryhisner who was thinking it was K.

I believe it is S:A484T. Omicron has A23013C (S:E484A), and then JH.2 gets G23012A which changes amino acid A (GCA) to T (ACA).

it has also the reversion! it is AAA so it is K please merge! cc @AngieHinrichs @ryhisner

wait still no PR! doing it now.
Schermata 2023-09-03 alle 11 45 43

@FedeGueli
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@AngieHinrichs created : #2247

@ryhisner
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I believe it is S:A484T. Omicron has A23013C (S:E484A), and then JH.2 gets G23012A which changes amino acid A (GCA) to T (ACA).

I think Usher masks the C23013A reversion. On each of three recent A484K proposed lineages, it misses C23013A, so the trees end up looking very strange. In addition to this BQ.1.2.2 lineage, you can see it in the trees for both lineages below (one of which has been designated).

sars-cov-2-variants/lineage-proposals#546
sars-cov-2-variants/lineage-proposals#232

On the topic of masked mutations, S:L5F is an extremely homoplasic mutation, but it never shows up on Usher. I have no reason to think it's not real. I think it's somewhat similar to S:L18F in much earlier lineages—a C->T mutation with an ideal APOBEC context (two T's on either side) that likely assists T-cell evasion in a certain percentage of HLA types (hence why they never grow beyond a small percentage). I feel pretty certain S:L5F is real.

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Oh my gosh, I apologize @FedeGueli for not checking my masking first, and @ryhisner you are totally right, I do mask C23013A in XBB although that's looking like a bad idea these days.

On the topic of masked mutations, S:L5F is an extremely homoplasic mutation

Yes, so much so that it was added to the Problematic Sites set pretty early on! So since the beginning of the UShER tree (2021) it has been masked before sequences are added to the tree.

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